Welcome

Welcome to my professional webpage.
I am a Computational Biologist affiliated with CINTESIS at the University of Algarve in Faro, Portugal.

Here you will find more about my Academic CV, my Scientific journey and a bit about my hobbies and interests.



MyScience

My Science

I am a full time scientist, and curiosity is my main driver. I am passionate about Open Science and I am always keen on establishing new collaborations.

Academic Resume | I have a PhD in Medical Sciences from the Radboud Universiteit (Nijmengen, The Netherlands); a Masters degree in Oncology by ICBAS - Universidade do Porto (Portugal); and a Bachelor degree in Applied Biology by Universidade do Minho Braga (Portugal). I have published over 27 articles in international journals, developed several RData packages as well as other software tools for the biomedical research community.

Work | I use Computational Biology/Bioinformatics as a way of answering biologically relevant questions. I have used OMICs datasets to study the genetic regulation of cancer, early vertebrate embryo development, stem cell differentiation, and mitochondrial evolution.

Interests | My research interests are focused on understanding how gene expression profiles translate into robust genetic modules that explain the phenotypic plasticity observed in healthy and diseased cells, particularly in cancer. Such knowledge holds the promise to better explain the molecular mechanisms underlying cancer biology.


CACAU Project | Cancer causality for precision oncology


DEvoCancer Project | Differential Allelic Expression in Breast Cancer mutations


ClockOME Project | microRNA regulation of the vertebrate embryo molecular clock


SPLICE Project | Alternative splicing in cardiomyogenesis


My PhD Project | The alternative evolutionary fates of mitochondrial proteins

MyCV

Isabel Duarte (PhD) - Junior Researcher
Faculty of Sciences and Technology (building 8, room 3.14)
University of Algarve, Faro - Portugal
Phone: + 351 289 800 100 (extension 7177)
Institutional website: UAlg
Scientific profile: Google scholar | ORCID | CienciaVitae
Social media: LinkedIn
Contact me: giduarte at ualg dot pt


Academic degrees

2017

  • PhD in Medical Sciences | Radboud Universiteit (Nijmegen, The Netherlands)

2005-2006

  • PhD program in Computational Biology | Instituto Gulbenkian de Ciência (Oeiras, Portugal)

2006

  • Master in Oncology | Universidade do Porto (Porto, Portugal)

2003

  • BSc in Applied Biology | Universidade do Minho (Braga, Portugal)


Current position

2022 – present

  • Junior researcher | CINTESIS - Universidade do Algarve (Faro, Portugal) |
    CEEC Project | Causal Inference in Cancer | Research fellow contract
Previous positions

2019 – 2022

  • Bioinformatics researcher | CINTESIS - Universidade do Algarve (Faro, Portugal)
    FCT Project | DEvoCancer: Decoding breast cancer evolution through mutant allele differential expression signatures | Post-doc research contract

2018 – 2019

  • Invited Assistant Professor | Faculty of Medicine and Biomedical Sciences - Universidade do Algarve - Faro, Portugal
    Lecturer in Computational Biology

2016 – 2019

  • Bioinformatics researcher | CBMR - Universidade do Algarve - Faro, Portugal
    FCT Project | ClockOME: Gene Regulatory Network in Temporal Control of Mesoderm Specification | Research grant

2014 – 2015

  • Bioinformatics researcher | CBMR - Universidade do Algarve - Faro, Portugal
    FCT Project | SPLICE: Alternative splicing and its impact on molecular networks during stem cell differentiation | Research grant

2012 - 2013

  • Bioinformatics expert | Radboud University (The Netherlands) & University of Birmingham (United Kingdom) & University of Jena (Germany)
    European ERASysBio+ project | LINCONET: Modelling the gene regulatory network underlying lineage commitment in human Mesenchymal Stem Cells | Research grant

2005

  • Lab researcher | Thomas Jefferson University - Philadelphia, USA
    Daniel Baugh Institute for Functional Genomics and Computational Biology | Masters degree student

2002 –2005

  • Lab researcher | Instituto Português de Oncologia Francisco Gentil (IPO) - Porto, Portugal
    Molecular Pathology Lab | Masters degree student

2002-2004

  • Practical classes assistant | Universidade do Minho - Braga, Portugal
    Antropobiology course | Practical classes instructor


Skills & Competences

  • Informatics

    R (software environment for statistical computing and graphics) • Perl (scripting language) • Bash (Unix command processor shell) • MySQL (open source database) • Linux (Operating System)

  • Bioinformatics

    Data science • Next Generation sequencing (OMICs) • R/Bioconductor • BigData management • Statistics • Phylogenomics • Comparative genomics • Genome annotation

  • Natural languages

    Portuguese | Native language

    English | Full professional proficiency

Teaching

2018 - 2023 | Computational Biology

  • Masters in Biomedical Sciences | Faculty of Medicine and Biomedical Sciences - Universidade do Algarve - Faro, Portugal

2017 - present | RNA-seq | Invited Yearly Seminar

  • Masters in Oncobiology | Faculty of Medicine and Biomedical Sciences - Universidade do Algarve - Faro, Portugal

2017 - present | Metagenomics | Invited Yearly Seminar

  • Masters in Molecular and Microbial Biology | Faculty of Sciences and Technology - Universidade do Algarve - Faro, Portugal

2018 - 2019 | Bioinformatics

  • BSc in Biomedical Sciences | Faculty of Medicine and Biomedical Sciences - Universidade do Algarve - Faro, Portugal


Selected publications | Peer-reviewed Journals

  • Barata Tânia, Duarte Isabel, Futschik ME. Integration of Stemness Gene Signatures Reveals Core Functional Modules of Stem Cells and Potential Novel Stemness Genes. Genes. 2023. https://doi.org/10.3390/genes14030745

  • Lizelle Correia*, Ramiro Magno*, Joana M. Xavier, Bernardo P. de Almeida, Isabel Duarte, Filipa Esteves, Marinella Ghezzo, Matthew Eldridge, Chong Sun, Astrid Bosma, Lorenza Mittempergher, Ana Marreiros, Rene Bernards, Carlos Caldas, Suet-Feung Chin, Ana-Teresa Maia. Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant. NPJ Breast Cancer. 2022. (doi: https://doi.org/10.1038/s41523-022-00435-9)

  • Duarte Isabel*, Carraco G*, Andrade RP. gga-miRNOME, A microRNA-sequencing dataset from chick embryo development. Nature Scientific Data. 2022. (doi: https://doi.org/10.1038/s41597-022-01126-7)

  • Duarte Isabel*, Magno R*, Maia AT. quincunx: an R package to query, download and wrangle PGS Catalog data. Bioinformatics. 2021. (doi: https://doi.org/10.1093/bioinformatics/btab522)

  • José Matos, Isabel Matos, Manuela Calha, Pedro Santos, Isabel Duarte, Yameric Cardoso, and Maria L. Faleiro. Insights from Bacteroides Species in Children with Type 1 Diabetes. Microorganisms. 2021. (doi: https://doi.org/10.3390/microorganisms9071436)

  • Liber M, Duarte Isabel, Maia AT, Oliveira HR. The history of lentil (Lens culinaris subsp. culinaris) domestication and spread as revealed by Genotyping-by-Sequencing of wild and landrace accessions. Frontiers in Plant Science. 2021. (doi: https://10.3389/fpls.2021.628439)

  • Machado S, Silva A, De Sousa-Coelho AL, Duarte Isabel, Grenho I, Santos B, Mayoral-Varo V, Megias D, Sánchez-Cabo F, Dopazo A, Ferreira BI, Link W. Harmine and Piperlongumine Revert TRIB2-Mediated Drug Resistance. Cancers. 2020. (doi: https://doi.org/10.3390/cancers12123689)

  • Pais-de-Azevedo T, Magno R, Duarte Isabel and Palmeirim I. Recent advances in understanding vertebrate segmentation. F1000 Research. 2018. (PMID: 29416855)

  • Pinto JP, Machado RSR, Magno R, Oliveira DV, Machado S, Andrade RP, Bragança J, Duarte I and Futschik ME. StemMapper: a curated gene expression database for stem cell lineage analysis. Nucleic Acids Research. 2017. (PMID: 29045725)

  • Magno R, Duarte Isabel, Andrade RP and Palmeirim I. rdml: A Mathematica package for parsing and importing Real-Time qPCR data. BMC Research Notes. 2017. (PMID: 28606167)

  • Macedo JA, Schrama D, Duarte Isabel, Tavares E, Renaut J, Futschik ME, Rodrigues PM and Melo EP. Membrane-enriched Proteomic changes Associated with Prion protein expression during Neural Differentiation and in Neuroblastoma Cells. BMC Genomics. 2017. (PMID: 28431525)

  • Pinto E, Anselmo M, Calha M, Bottrill A, Duarte Isabel, Andrew PW and Faleiro ML. The Intestinal Proteome of Diabetic and Control children are Enriched with Different Microbial and Host proteins. Microbiology (UK). 2017. (PMID: 28270263)

  • van Zoelen EJ, Duarte Isabel, Hendriks JM and van der Woning SP. TGFB-Induced Switch from Adipogenic to Osteogenic Differentiation of Human Mesenchymal Stem Cells: Identification of drug targets for prevention of fat cell differentiation. Stem Cell Research & Therapy. 2016. (PMID: 27562730)

  • Pinto JP, Kalathur RK, Oliveira DV, Barata T, Machado RS, Machado S, Pacheco-Leyva I, Duarte Isabel and Futschik ME. StemChecker: a web-based tool to discover and explore stemness signatures in gene sets. Nucleic Acids Research. 2015. (PMID: 26007653)

  • Huynen MA, Duarte Isabel and Szklarczyk R. Loss, replacement and gain of proteins at the origin of the mitochondria. Biochimica et Biophysica Acta - Bioenergetics. 2013. (PMID: 22902511)

  • Willems P, Wanschers B, Esseling J, Szklarczyk R, Kudla U, Duarte Isabel, Forkink M, Nooteboom M, Swarts H, Gloerich J, Nijtmans L, Koopman W and Huynen MA. BOLA1 is an aerobic protein that prevents mitochondrial morphology changes induced by glutathione depletion. Antioxidants & Redox Signaling. 2013. (PMID: 22746225)

  • Kensche PR, Duarte Isabel and Huynen MA. A three-dimensional topology of complex I inferred from evolutionary correlation. BMC Structural Biology. 2012. (PMID: 22857522)

  • Duarte Isabel, Naaburs SB, Magno R and Huynen MA. Evolution and diversification of the organellar release factor family. Molecular Biology and Evolution. 2012. (PMID: 22688947)

  • Huynen MA, Duarte Isabel, Chrzanowska-Lightowlers ZM and Naaburs SB. Structure based hypothesis of a mitochondrial ribosome rescue mechanism. Biologyl Direct. 2012. (PMID: 22569235)

  • de Graaf RM, Ricard G, van Alen TA, Duarte Isabel, Dutilh BE, Burgtorf C, Kuiper JW, van der Staay GW, Tielens AG, Huynen MA, Hackstein JH. The organellar genome and metabolic potential of the hydrogen-producing mitochondrion of Nyctotherus ovalis. Molecular Biology and Evolution. 2011. (PMID: 21378103)

  • Duarte Isabel*, de Graaf RM*, van Alen TA, Kuiper JW, Schotanus K, Rosenberg J, Huynen MA, Hackstein JH. The hydrogenosomes of Psalteriomonas lanterna. BMC Evolutionary Biology. 2009. (PMID: 20003182)

  • Ricard G, de Graaf RM, Dutilh BE, Duarte Isabel, van Alen TA, van Hoek AH, Boxma B, van der Staay GW, Moon-van der Staay SY, Chang WJ, Landweber LF, Hackstein JH, Huynen MA. Macronuclear genome structure of the ciliate Nyctotherus ovalis: single-gene chromosomes and tiny introns. BMC Genomics. 2008. (PMID: 19061489)

  • Santos AM, Sousa H, Pinto D, Portela C, Pereira D, Catarino R, Duarte Isabel, Lopes C, Medeiros R. Linking TP53 codon 72 and P21 nt590 genotypes to the development of cervical and ovarian cancer. European Journal of Cancer. 2006. (PMID: 16542834)

  • Duarte Isabel, Santos AM, Sousa H, Catarino R, Pinto D, Matos A, Pereira D, Moutinho J, Canedo P, Machado JC, Medeiros R. G-308A TNF-alpha Polymorphism is Associated with an Increased Risk of Invasive Cervical Cancer. Biochemical and Biophysical Research Communications. 2005. (PMID: 16009345)

Pre-print publications

  • Ana Cristina Maia-Fernandes, Ana Martins-Jesus, Tomás Pais-de-Azevedo, Ramiro Magno, Isabel Duarte, Raquel P. Andrade. Spatio-Temporal Dynamics of Early Somite Segmentation in the Chicken Embryo. bioRxiv. 2023. (doi: https://doi.org/10.1101/2023.04.05.535703)

  • Duarte Isabel*, Liber M*, Magno R, Andrade RP. FrozenChicken: Promoting the meta-analysis of chicken microarray data. bioRxiv. 2021. (doi: https://doi.org/10.1101/2021.02.25.432894)

  • Duarte Isabel and Huynen MA. Contribution of Lateral Gene Transfer to the evolution of the eukaryotic fungus Piromyces sp. E2: Massive bacterial transfer of genes involved in carbohydrate metabolism. bioRxiv. 2019. (doi: https://doi.org/10.1101/514042)


Software packages & Open code
Datasets | Published, Managed & Analysed


* Equal contribution

MyHobbies

About Me

I love to read, to play ukulele, to think, to learn and to teach, to discuss new ideas, and to engage in outdoors activities with my friends.

I regularly organize get-together evenings of relaxed scientific discussions or board game nights, over tea and homemade cake.

I love animals (except for spiders… I hate spiders!). I like music, cinema, books, writing, sewing, digital painting, puzzles, science toys and gadgets, and everything pink. I like nonsense humor, and chocolate. I am sociable and always keen on tackling new challenges.

Others describe me as creative, curious, upbeat and reliable. I see myself as transparent.


Outreach

I am a strong believer that knowledge is power, so I always try to empower others by sharing my scientific knowledge and enthusiasm for science and technology. Here are some of my outreach projects.


Outreach projects & Volunteering
  • Pattern Institute | Non-profit organization | Board member [2023-present]

The Pattern Institute is a non-profit association, whose mission is science promotion and outreach.


  • Byte Club | Science outreach for graduate students | Founding member [2018-2021]

The Byte Club is a relaxed scientific club created by myself and Ramiro Magno in 2018, to discuss science with graduate students and other researchers, over coffee and cake. The meetings are free and open to all the academic community.

Before the COVID-19 pandemic the meetings took place on the first Thursday of each month, at Universidade do Algarve (Building 8, 3rd floor). The members take turns in choosing the topic of discussion for the next meeting. During the COVID-19 confinement in 2020, the meetings have been held online.


  • Collaboratorium | Non-profit organization | Founding member & Volunteer [2013-2014]

Collaboratorium was a volunteering project that I started in Portugal (Vermoim, Vila Nova de Famalicão). It aimed at fostering community cohesion and collaboration around shared interests, specifically targeting young children to combat the persistently high school dropout rates in the region, particularly among girls. This initiative aided them in their studies, while also implementing engaging activities designed to increase their interest in science and technology.


  • Scientific outreach for the general public

I love science & I love to write. This section showcases some of the results when these two passions collide.



  • Between 2007 and 2008, I wrote a science column for the portuguese newspaper Diário do Minho. These are the 3 most shared texts (in Portuguese only).


  • European Association for Cancer Research Ambassador [2021-present]

I am a proud cancer researcher, ambassador member of the European Association for Cancer Research (EACR).